A social justice bench of justices M B Lokur and U U Lalit said the ministry had taken three adjournments since 2014 in the matter.
It also brushed aside the ministry's submission that the file for the appointment of Chairman, a post lying vacant for the past one and half years, was lying in the Prime Minister's Office (PMO).
The bench imposed the fine on the ministry observing that failure to appoint the chairman was an "unexplained delay".
"We do not know. We are not concerned. It cannot take one and a half years to appoint NCPCR Chairman. You speak to the PMO", it said after the ASG tried to stress upon the bench about the intricacies involved in the appointment process.
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It asked the counsel to go through its three earlier orders saying, "If you do not accept an appointment, then reject it" but take a decision.
"This is just too much. You are not going to do anything as the High court is doing it," the bench said after which counsel for UP government regretted to the sentence written in the affidavit and offered to amend it.
The court has now fixed the matter for September 18.